Sorry, I kept meaning to reply this, but I don't really seem to have the time for effortposts here that I used to lately.
I guess I was being a bit reductive when I said not to expect them to make Venat a villain; like you point out, I've said in the past the past that that's not even what I want, and just wanted her character to be portrayed as a morally grey figure. In this context, though, I was using 'villain' less as 'someone depicted as morally bad' and more as 'antagonist'. For all I disliked it, Endwalker went so hard on Hydaelyn being heroic and in the right that flipping the framing outright to the Scions all admitting her actions were kinda wrong and a better solution should have been found would create a dissonance in the script, where how the player was signaled to emotionally respond would flip sharply after a relatively short amount of gameplay. That kind of thing is something I'd assume game writers are eager to avoid, since most people have a fairly superficial investment in the plot, making consistency much more important than the actual message.
It's frustrating, but though it feels likely from the interviews and the Omega questline that the Venat arc came out a little strange and absolutist, the only real ways they can respond to that without making a mess of the story is to either 'phase out' the entire question by negating the tension between the canonical tone of the Sundering plot and the actual facts (either by making the Sundering less bad, which they seem averse to, or having the Ancients survive in some way) or to push it into side-content where it won't force established characters to contradict their own positions. I doubt they'll touch Amaurot in the MSQ again in the medium term; maybe eventually we can hope for a proper revisit to it, in the way that ultimately happened with a lot of the beastmen stuff.
It's painful to have to accept the disproportionate nature of the situation, where any addendums still have to exist in deference to the vibe of the major release that just happened. But for the time being, I'm reassured just by the fact that the writers are obviously not married to it.
Like I said, Mide and her boyfriend get the knowledge of Alexander from a time paradox; they don't come up with it themselves, they learn about it from ancient Hotgo lore that in turn comes from them that in turn comes from ancient Hotgo lore... Etc. It's an obnoxious way to do time travel writing, IMO; no better here than in EW's core plot.
You're right that they also get insight from Omega, but that also isn't technology they're coming up with themselves. So again, time travel can't really be framed as an instance of the Sundered being superior to the Unsundered, when what it really comes down to isn't just ingenuity, but knowledge from a specific group of aliens.